Development of next-generation sequencing (NGS)-based SSRs in African nightshades: Tools for analyzing genetic diversity for conservation and breeding

Ronoh, Regina; Linde, Marcus; Winkelmann, Traud; Abukutsa‐Onyango, Mary; Dinssa, Fekadu F.; Debener, Thomas

doi:10.1016/j.scienta.2018.03.003

Cited by 7 publications

(4 citation statements)

References 50 publications

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“…Development of SSR markers of R. chinensis and S. chinensis SSR markers have been widely developed in plants for genetic diversity analysis, parentage assessment, species identification, and genetic map constructions [31][32][33][34][35]. Since no reference genome is available for R. chinensis, the transcriptome and reduced-representation genomes were used to develop SSRs in this study.…”

Section: Discussionmentioning

confidence: 99%

Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

Tian,

Sang,

Lan

et al. 2023

BMC Plant Biol

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Background Galla chinensis is a traditional Chinese medicine (TCM) produced due to the interaction between the Fordinae aphids and the Rhus plant species. Horned galls with high tannin content are the most widely cultivated gall type, and Wufeng county of Hubei province in China is the center of cultivation. However, long-term artificial cultivation and domestication of horned galls to meet the increasing production demand have led to quality degradation. Understanding the reasons underlying quality degradation is urgent for horned gall production and application. The present study used a combination of metabolic, genetic, and ecological analyses to investigate the quality and genetic differentiation of the horned galls under long-term domestication as well as the potential relationships between them. Results Analysis of gallic acid content and other three phenotypic traits (fresh weight, gall size, and wall thickness) revealed quality differentiation of horned galls collected from five locations in Wufeng, in which the cultivated samples from Wang Jiaping (WJP) showed the highest degradation. Genetic differentiation between the cultivated and wild Rhus chinensis trees in WJP, and between WJP and the other populations was detected based on SSR molecular markers, however, no significant difference in genetic structure was seen for the aphid populations. Among the various ecological factors examined, temperature was identified as the primary one affecting the quality of horned galls. Conclusions Both genetic and ecological factors caused quality differentiation of horned galls. The collection of diverse germplasm of host trees and aphids will help reduce the quality degradation of horned galls in Wufeng.

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Section: Discussionmentioning

confidence: 99%

Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

Tian,

Sang,

Lan

et al. 2023

BMC Plant Biol

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“…Traditional microsatellite marker development is time-consuming and labor-intensive, and the development of next-generation sequencing (NGS) technology provides a more economical and convenient method. RNA sequencing (RNA-Seq) is a high-throughput NGS-based technology that has great advantages in mining microsatellites and has good applications in numerous species [27][28][29].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity Evaluation and Population Structure Analysis of Red Swamp Crayfish (Procambarus clarkii) from Lakes and Rice Fields by SSR Markers

Guo

Liu

Zhou

et al. 2022

Fishes

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The red swamp crayfish (Procambarus clarkii) is an important aquatic animal and has developed as a popular aquaculture species in China. In this study, a total of 72,839 SSR motifs were identified from transcriptional data, and 20 microsatellite markers of them were finally developed to assess the genetic diversities of seven wild populations from natural lakes and nine cultured populations from rice fields. Genetic diversity was slightly higher in the cultured populations than in the wild populations. The degree of genetic differentiation between cultured populations is slight, while a moderate to a large degree of genetic differentiation between wild populations and most of the variations occurred within individuals (79%). The analysis of cluster, principal coordinate analysis and STRUCTURE were similar, and they showed that isolation-by-distance pattern was not significant. The microsatellite markers developed in this study can not only be used for genetic monitoring of population but also provide important information for the management of breeding and cultured population in red swamp crayfish.

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“…With the improvement of next generation sequencing technology (NGS), RNA sequencing has gradually become a convenient and efficient technique for detecting SSR markers and has been extensively applied in numerous species [21, 22]. Given the limited genetic studies, SSRs would be the most abundant resources for genetic diversity analysis, cultivar identification and marker-assisted breeding of C .…”

Section: Introductionmentioning

confidence: 99%

SSR marker development in Clerodendrum trichotomum using transcriptome sequencing

et al. 2019

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Clerodendrum trichotomum, a member of the Lamiaceae (Verbenaceae) family, is an ornamental plant widely distributed in South Asia. Previous studies have focused primarily on its growth characteristics, stress resistance, and pharmacological applications; however, molecular investigations remain limited. Considering germplasm conservation and the extensive applications of this plant, it is necessary to explore transcriptome resources and SSR makers for C. trichotomum. In the present study, RNA sequencing was used to determine the transcriptome of C. trichotomum. Subsequently, unigene annotations and classifications were obtained, and SSRs were mined with MIcroSAtellite. Finally, primer pairs designed with Oligo 6.0 were selected for polymorphism validation. In total, 127,325,666 high-quality reads were obtained, and 58,345 non-redundant unigenes were generated, of which 36,900 (63.24%) were annotated. Among the annotated unigenes, 35,980 (97.51%) had significant similarity to 607 species in Nr databases. In addition, a total of 6,444 SSRs were identified in 5,530 unigenes, and 200 random primer pairs were designed for polymorphism validation. Furthermore, after primary polymorphism identification, 30 polymorphic primer pairs were selected for the further polymorphism screening, and 200 alleles were identified, 197 of which showed polymorphism. In this work, a large number of unigenes were generated, and numerous SSRs were detected. These findings should be beneficial for further investigations into germplasm conservation and various applications of C. trichotomum. These results should also provide a solid foundation for future molecular biology studies in C. trichotomum.

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Development of next-generation sequencing (NGS)-based SSRs in African nightshades: Tools for analyzing genetic diversity for conservation and breeding

Cited by 7 publications

References 50 publications

Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

Fine-Scale analysis of both wild and cultivated horned galls provides insight into their quality differentiation

Genetic Diversity Evaluation and Population Structure Analysis of Red Swamp Crayfish (Procambarus clarkii) from Lakes and Rice Fields by SSR Markers

SSR marker development in Clerodendrum trichotomum using transcriptome sequencing

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